Adult patients with Klinefelter syndrome (KS) are characterized by a highly variable phenotype including tall stature, obesity and hypergonadotropic hypogonadism as well as an increased risk of developing insulin resistance, metabolic syndrome, and osteoporosis. Most adults need testosterone replacement therapy (TRT), whereas the use of TRT during puberty has been debated. In this retrospective, observational study reproductive hormones and whole-body dual-energy X-ray absorptiometry (DXA) derived body composition and bone mineral content were standardized to age-related standard deviation scores (SDS) in 62 patients with KS aged 5.9 to 20.6 years. Serum concentrations of total testosterone and inhibin B were low, whereas LH and FSH were high in patients before TRT. Despite normal body mass index (BMI), body fat% and ratio between android fat% and gynoid fat% were significantly higher in the entire group irrespective of treatment status. In patients evaluated before and during TRT a tendency towards a more beneficial body composition with a significant reduction in ratio between android fat% and gynoid fat% during TRT was found. Bone mineral content (BMC) did not differ from the reference, but BMC corrected for bone area was significantly lower when compared to the reference. This study confirms that patients with KS have an unfavorable body composition and an impaired bone mineral status already during childhood and adolescence. Systematic studies are needed to evaluate whether TRT during puberty will improve these parameters.